DRought Impacts on soil microbial metabolism in European foRests (DRIER)

Soil is a critical storage pool for carbon in Earth’s surface. How carbon cycling will change in soils as a result of anthropogenic climate forcing remains unclear, in part because of limited mechanistic understanding of how microbial metabolism and diversity combine to affect carbon portioning between microbial biomass and respiration (known as carbon use efficiency or CUE). In central Europe, increased drought frequency and intensity is likely to impact carbon cycling and CUE in soils in the near future, due to changes in the availability of organic matter as moisture content decreases, and to changes in the composition of organic matter input from plants. To improve our process-based understanding of how carbon cycling will change in the soils of central European forests under drought, I propose to develop and apply a novel tool to quantify changes in the central carbon metabolism of soil microbial communities, based on compound-specific hydrogen isotope measurements of phospholipid-derived fatty acids (PLFAs), which are contained in the lipid membranes of living microbes.

Studies with cultured microbes have demonstrated that the hydrogen isotope composition of lipids is highly sensitive to central metabolism, with lipids produced from tricarboxylic acid cycle precursors and intermediates having d²H values that are up to 250 ‰ higher than those from sugar-based metabolisms. Lipid d²H values thus have great potential as indicators of the activity of central metabolic pathways, but have thus far only been employed in aquatic settings and microbial mats, not in soils.

In DRIER, I will initially test the suitability of d²H values of PLFAs as a proxy for net soil microbial metabolism through a series of increasingly complex laboratory experiments beginning with simple co-cultures inoculated with two model bacterial species and progressing to small mesocosms of natural microbiomes from local forest soils. I will then conduct several larger soil mesocosm experiments, evaluating how the metabolism and substrates used by different microbial groups change under drought, and how these changes are influenced by the presence of living plant roots or leaf litter additions. In addition to measuring d²H values of PLFAs from these mesocosms, I will characterize changes in the quality of soil organic matter and the abundance of specific metabolites through high-resolution mass spectrometry, changes in the microbial community composition through 16S amplicon sequencing, and changes in microbial gene expression through metatranscriptomic analyses. Finally, I will determine how soil microbial metabolism changes during a long-term water exclusion experiment in a natural forest at the Swiss Canopy Crane II site in Hölstein, BL. I will collect soil cores at multiple time points from drought and control plots and apply the approach developed in the soil mesocosms to assess shifts in microbial metabolism in response to sustained, multi-year droughts and place these shifts in the context of long-term changes is soil respiration and CUE. I will also conduct full metagenomic analyses from the soil cores to determine how long-term drought affects overall soil microbial community structure, and how this impacts the overall CUE potential of soils over time. Through this cutting-edge, combined multi-omics approach, DRIER will reveal unique insights about the interactions of soil organic matter and microbial metabolism during drought in central European forests and will likely establish PLFA d²H values as a novel, integrated proxy for central metabolism in soil microbes at the community level.